1-55125114-CTT-C

Position:

• chr1-55125114-CTT-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_015306.3(USP24):​c.3960+204_3960+205del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (35669 hom., cov: 0)
• Consequence: USP24 NM_015306.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

USP24 (HGNC:12623): (ubiquitin specific peptidase 24) Modification of cellular proteins by ubiquitin is an essential regulatory mechanism controlled by the coordinated action of multiple ubiquitin-conjugating and deubiquitinating enzymes. USP24 belongs to a large family of cysteine proteases that function as deubiquitinating enzymes (Quesada et al., 2004 [PubMed 14715245]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USP24	NM_015306.3	c.3960+204_3960+205del		intron_variant		ENST00000294383.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP24	ENST00000294383.7	c.3960+204_3960+205del		intron_variant		5	NM_015306.3	P1
USP24	ENST00000484447.6	c.3960+204_3960+205del		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99098 AN: 151718 Hom.: 35660 Cov.: 0

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.716

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.653 AC: 99120 AN: 151838 Hom.: 35669 Cov.: 0 AF XY: 0.662 AC XY: 49106 AN XY: 74198

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.720

Alfa AF: 0.590 Hom.: 2051

Bravo AF: 0.642

Asia WGS AF: 0.840 AC: 2922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2307832; hg19: chr1-55590787;